NPASS Compound

Structure

NPC325839 OpenBabel06302215232D 26 31 0 0 1 0 0 0 0 0999 V2000 0.8837 -0.3893 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6758 0.1824 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.6857 1.5540 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 1.4780 2.1259 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3617 1.7366 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4680 0.7543 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.3607 0.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2069 0.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0531 0.3569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0531 -0.6202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2069 -1.1088 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3607 -0.6202 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9824 -0.9222 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5567 -0.1317 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6274 -0.4336 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1063 0.9823 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9987 1.3796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4871 0.5336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4639 0.5336 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9523 1.3796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4639 2.2255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4871 2.2255 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9078 1.1765 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0099 0.2050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3563 0.9309 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 17 1 0 0 0 0 1 2 1 0 0 0 0 2 6 1 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 16 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 7 12 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 9 15 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 10 13 1 0 0 0 0 11 12 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 18 23 1 0 0 0 0 18 19 2 0 0 0 0 19 20 1 0 0 0 0 20 26 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 21 24 1 0 0 0 0 22 23 2 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	354.11
Volume:	340.06
LogP:	3.066
LogD:	2.918
LogS:	-5.868
# Rotatable Bonds:	2
TPSA:	55.38
# H-Bond Aceptor:	6
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.825
Synthetic Accessibility Score:	3.774
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.033
MDCK Permeability:	6.124360515968874e-05
Pgp-inhibitor:	0.985
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.002
30% Bioavailability (F30%):	0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.173
Plasma Protein Binding (PPB):	97.52722930908203%
Volume Distribution (VD):	1.163
Pgp-substrate:	2.7944552898406982%

ADMET: Metabolism

CYP1A2-inhibitor:	0.52
CYP1A2-substrate:	0.284
CYP2C19-inhibitor:	0.95
CYP2C19-substrate:	0.382
CYP2C9-inhibitor:	0.677
CYP2C9-substrate:	0.858
CYP2D6-inhibitor:	0.952
CYP2D6-substrate:	0.915
CYP3A4-inhibitor:	0.963
CYP3A4-substrate:	0.521

ADMET: Excretion

Clearance (CL):	17.15
Half-life (T1/2):	0.062

ADMET: Toxicity

hERG Blockers:	0.148
Human Hepatotoxicity (H-HT):	0.181
Drug-inuced Liver Injury (DILI):	0.41
AMES Toxicity:	0.713
Rat Oral Acute Toxicity:	0.194
Maximum Recommended Daily Dose:	0.508
Skin Sensitization:	0.27
Carcinogencity:	0.894
Eye Corrosion:	0.003
Eye Irritation:	0.153
Respiratory Toxicity:	0.188

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC325839

Natural Product ID:	NPC325839
*Common Name:**	PEYUIKBAABKQKQ-NILVNCKXSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PEYUIKBAABKQKQ-NILVNCKXSA-N
Standard InCHI:	InChI=1S/C20H18O6/c1-3-15-17(25-9-23-15)5-11(1)19-13-7-22-20(14(13)8-21-19)12-2-4-16-18(6-12)26-10-24-16/h1-6,13-14,19-20H,7-10H2/t13-,14-,19?,20?/m0/s1
SMILES:	C1C2C(COC2C3=CC4=C(C=C3)OCO4)C(O1)C5=CC6=C(C=C5)OCO6
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10882750
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0003686] Furanoid lignans

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	leaf	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1007/s11418-006-0112-9]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	seed	n.a.	PMID[11540412]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	leaf	n.a.	PMID[11816040]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15388977]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16872768]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[17125224]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	stem	n.a.	PMID[17202689]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[17625893]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[18293924]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	stem bark	n.a.	n.a.	PMID[18303853]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	Stems; Barks	n.a.	n.a.	PMID[18303853]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20192247]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[20628994]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	fruits	n.a.	n.a.	PMID[20839888]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	fruit	n.a.	PMID[21319773]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	roots	n.a.	n.a.	PMID[22381047]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[22445674]
NPO30633	Acanthopanax sessiliflorus	n.a.	n.a.	n.a.	Fruits	n.a.	n.a.	PMID[22691179]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23434420]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23623680]
NPO29744	Acanthopanax gracilistylus	n.a.	n.a.	n.a.	Root Bark	n.a.	n.a.	PMID[25338180]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	fruits	n.a.	n.a.	PMID[25735399]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28322565]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[28968119]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	Barks	Iksan, Chunbuk, Korea	n.a.	PMID[3127544]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6387056]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO29744	Acanthopanax gracilistylus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO20362	Ruta montana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3404	Magnolia mutabilis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO542	Artemisia absinthium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO30633	Acanthopanax sessiliflorus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3404	Magnolia mutabilis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO542	Artemisia absinthium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20362	Ruta montana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO30633	Acanthopanax sessiliflorus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO31494	Acanthopanax senticosus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12468.2	Asarum heterotropoides f. schm. var. mandshuricum (maxim.) kitag.	Varieties	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3404	Magnolia mutabilis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20362	Ruta montana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO542	Artemisia absinthium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29744	Acanthopanax gracilistylus	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO22079	Paulownia tomentosa	Species	Paulowniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1382	Hyptis tomentosa	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26237	Piper longum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9290	Zanthoxylum piperitum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3404	Magnolia mutabilis	Species	Magnoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6336	Asarum sieboldii	Species	Aristolochiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20362	Ruta montana	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26589	Artemisia annua L.	Strain	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24778	Sesamum orientale	Species	Pedaliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9650	Zanthoxylum nitidum	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO542	Artemisia absinthium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC325839 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC325839 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data